The conductance of single molecule junctions is calculated using a Landauer approach combined with many-body perturbation theory to account for electron correlation. Contrary to intuition, a mere correction of the density-functional theory eigenvalues is found not to affect noticeably the zero-bias conductance. To improve the agreement with experiments, it is necessary to go beyond this standard procedure by also updating the wave functions. This leads to both the reduction of the molecular character and the increase of the e(g)(d(z)2) character on gold atoms around the Fermi energy.